bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/hgSessionHelp.html src/hg/htdocs/goldenPath/help/hgSessionHelp.html index e950f0c7d94..41cbfe8f635 100755 --- src/hg/htdocs/goldenPath/help/hgSessionHelp.html +++ src/hg/htdocs/goldenPath/help/hgSessionHelp.html @@ -587,46 +587,46 @@ <a href="/FAQ/FAQformat.html#format1.5" target="_blank">bigBed</a>, <a href="/FAQ/FAQformat.html#format6" target="_blank">WIG</a>, <a href="/FAQ/FAQformat.html#format6.1" target="_blank">bigWig</a>, and <a href="/FAQ/FAQformat.html#format10.1" target="_blank">VCF</a> data types. The last attribute, <strong>bigDataUrl</strong>, is required for remotely hosted data types such as <a href="../help/bam.html" target="_blank">BAM</a>, <a href="../help/cram.html" target="_blank">CRAM</a>, <a href="../help/bigBed.html" target="_blank">bigBed</a>, <a href="../help/bigWig.html" target="_blank">bigWig</a>, and <a href="../help/vcf.html" target="_blank">VCF</a>.</p> <p> Adding more <a href="customTrack.html#TRACK">attribute=value</a> pairs can further customize the display. Here is a custom track that uses the <strong>visibility</strong> and <strong>description</strong> atrributes: -<pre><code>track type=bam visibility=dense name="My BAM" description="Example from the ENCODE RNA-seq CSHL track" bigDataUrl=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqA549CellPapAlnRep1.bam</code></pre></p> +<pre><code>track type=bam visibility=dense name="My BAM" description="Example from the ENCODE RNA-seq CSHL track" bigDataUrl=http://hgdownload.gi.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqA549CellPapAlnRep1.bam</code></pre></p> <p> There are also options to <a href="hgBamTrackHelp.html">configure the display</a> of your BAM files, such as a <em>density plot feature</em> that will dynamically process the underlying BAM into a wiggle signal.</p> <hr> <h6>bigWig custom track</h6> <p> A bigWig file is useful when trying to display dense, continuous data. Read more on the <a href="bigWig.html">bigWig track format</a> help page. Here is an example bigWig track that is colored red, instead of the default black color, that can be pasted directly into the <a href="../../cgi-bin/hgCustom">Custom Tracks Page</a>: -<pre><code>track color=255,0,0 name="HeLa-S3 nucleus minus signal" description="RNA Subcellular CAGE Localization from ENCODE/RIKEN" type=bigWig visibility=full bigDataUrl=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHelas3NucleusPapMinusSignalRep1.bigWig</code></pre></p> +<pre><code>track color=255,0,0 name="HeLa-S3 nucleus minus signal" description="RNA Subcellular CAGE Localization from ENCODE/RIKEN" type=bigWig visibility=full bigDataUrl=http://hgdownload.gi.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHelas3NucleusPapMinusSignalRep1.bigWig</code></pre></p> <p> There are also options to <a href="hgWiggleTrackHelp.html">configure the display</a> of your wiggle tracks, such as changing the track height or type of graph.</p> <!-- ====Creating a session====================== --> <a name="NAR_session"></a> <h3>Creating a session for NAR publications</h3> <p> After creating your custom tracks and viewing your data on the Genome Browser, you can save all of your tracks and settings to a snapshot of the Genome Browser called a <em>session</em>. You can easily save a session by following these five steps:</p> <ol> <li> <strong>Configure the Genome Browser to your preference</strong><br> @@ -722,18 +722,18 @@ hosted. This will require the use of a web-accessible location to load the track hub in the UCSC Genome Browser. If your institution does not provide web space for you, you can look into hosting your binary files at a couple different web hosting services, such as <a href="http://www.cyverse.org/">CyVerse</a> or <a href="https://figshare.com/">figshare</a>. If you would like to learn more about using track hubs, please read our <a href="hgTrackHubHelp.html">Track Hub help page</a>.</p> <!-- ====Genome Browser inquiries================ --> <h3>Genome Browser inquiries</h3> <p> If you have any questions regarding the creation of your custom track or session, please feel free to <a href="../../contacts.html">contact us</a>. Before submitting a question, we strongly encourage you to search our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a>, our <a href="../../FAQ">website</a>, and our -<a href="http://genomewiki.soe.ucsc.edu/index.php/Main_Page">wiki</a> for the answer. +<a href="http://genomewiki.gi.ucsc.edu/index.php/Main_Page">wiki</a> for the answer. <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->